OROCHI Report

All the figures and tables contained in this report are available with publication-ready quality in the output directory of the OROCHI user.

For each of the sections shown in this report, these are the data used:

• Read-based: Quality-controlled shotgun sequencing reads
• Contig-based: Assemblies
• Bin-based: Refined and de-replicated bins

Read-based

*All read-based plots were made using MicrobiotaProcess. For more information, consult their documentation.

Alpha diversity

1. Observed and Shannon indexes for all samples, regardless of treatment
2. Boxplot and violin plot of Observed and Shannon indexes per treatment @Todo: add pannel labeling

Taxonomic abundance

Average read counts per treatment plotted per taxonomic level

For all the samples, using a heatmap maybe be a better option to plot all this information in a more understandable way. Columns correspond to samples, rows correspond to t

Beta diversity

Clustering

Bin-based

CheckM results

MAG linkage